Is there any way to reset the speedometer so that it will read the correct speed? I don't have the 12" tires I have 13" ones. I used my GPS to see how far off from the actual reading I was. It turns out that it's about 3.5-5 miles off from the actual speed. So if it says that I'm going 35, I'm actually going nearly 40.

You'll need to either swap transmissions or tear your transmission down completely to get to the drive gear for the speedometer. Not worth the trouble if you ask me. 95 and up cars came with 13" wheels so the transmission would have the proper drive for your speedometer, but they don't come in the same gear ratio that your current transmission has, so you'd be introducing another change.